Patient I-H-108333

View Patient in Leukgen

Individual DMP ID: P-0006237

Gender: MALE

Disease(s): UNDIFFERENTIATED SARCOMA (UNDIFS)

Part C Consent: True

Number of WGS Samples: 1

Number of RNAseq Samples: 1

CBio Portal Results:

Tumor_Sample_Barcode	Chromosome	Start_Position	Reference_Allele	Tumor_Seq_Allele2	Hugo_Symbol	VAF	Variant_Classification	HGVSp_Short
P-0006237-T04-IM6	3	178917478	G	A	PIK3CA	0.270423	Missense_Mutation	p.G118D

RNA Sample: I-H-108333-T2-1-R1-1

Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

Tissue Site: R Gluteal Mass

Days since birth at collection: 8029

Fusion Results:

High Confidence Fusions:

GENE1	GENE2	DESCRIPTION	SPAN_READS	SPLIT_READS	LEFTBREAK	RIGHTBREAK	CALLER_EFFECT	ANNOT_EFFECT	CALLER	NUM_CALLERS
MGA	NUTM1	oncogene,cancer,exon-exon	14	19	15:42054560:+	15:34640170:+	in-frame	in-frame	FUSIONCATCHER	3

GENE1	GENE2	DESCRIPTION	SPAN_READS	SPLIT_READS	LEFTBREAK	RIGHTBREAK	CALLER_EFFECT	ANNOT_EFFECT	CALLER	NUM_CALLERS
IGH@	IL3RA	known,cancer,m0,multi	3	1	14:106913401:-	X:1449932:+	---/intergenic	---/intergenic	FUSIONCATCHER	1

View RNAFUSIONS Report

Expression TSNE Results:

Bokeh Application

Overexpressed Cancer Genes:

Gene	Log Fold Change	Loc	Cancers
NUTM1	7.61806	15q14	lethal midline carcinoma
OLIG2	4.29052	21q22.11	T-ALL
MLF1	3.65278	3q25.1	AML
LRIG3	2.29114	12q14.1	NSCLC
SFRP4	2.16084	7p14.1	colorectal cancer, melanoma, SCC, gastric cancer, oesophageal SCC

WGS Sample: I-H-108333-T2-2-D1-1

Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

Tissue Site: R Gluteal Mass

Days since birth at collection: 8029

Normal used: I-H-108333-N2-1-D1-1

Median Coverage: 115

MSISensor HAS NOT BEEN RUN

Copy Number Results:

Tumor Purity: 0.9

Tumor Ploidy: 2.24

No Amplifications or Homozygous losses for Oncogenes or TSGs

SNV Results:

SNV Likely Drivers:

CHR	START	GENE	EFFECT	cDNA_CHANGE	PROTEIN_CHANGE	TARGET_VAF	REFERENCE_VAF	REFERENCE_DEPTH	Oncogene	TSG	CCF	GENE_TPM
3	178917478	PIK3CA	non_synonymous_codon	c.353G>A	p.G118D	0.35	0	37	✔		0.785316	9.70179

CHR	START	GENE	EFFECT	cDNA_CHANGE	PROTEIN_CHANGE	TARGET_VAF	REFERENCE_VAF	REFERENCE_DEPTH	Oncogene	TSG	CCF	GENE_TPM
1	35657838	SFPQ	non_synonymous_codon	c.813G>C	p.K271N	0.42	0	43		✔	0.930745	77.7173
1	43213986	LEPRE1	non_synonymous_codon	c.1723G>T	p.V575F	0.37	0	42			0.843369	17.4142
2	103321091	SLC9A2	non_synonymous_codon	c.1934G>A	p.R645Q	0.42	0	47			0.924928	1.04438
2	128263132	IWS1	non_synonymous_codon	c.347A>G	p.H116R	0.41	0	31			0.957338	8.2394
2	161052875	ITGB6	non_synonymous_codon	c.198A>T	p.L66F	0.43	0	39			0.96284	1.06111
2	170050292	LRP2	non_synonymous_codon	c.8809G>A	p.E2937K	0.39	0	45			0.859149	0.014024
2	174820961	SP3	splice_site_variant	c.280-1G>A	p.?	0.42	0	27			0.948306	19.1651
3	7456718	GRM7	non_synonymous_codon	c.1042G>A	p.A348T	0.45	0	39			0.994606	0.444721
3	178917478	PIK3CA	non_synonymous_codon	c.353G>A	p.G118D	0.35	0	37	✔		0.785316	9.70179
4	57344789	SRP72	non_synonymous_codon	c.799G>A	p.A267T	0.48	0	44			1.0941	22.1599
4	135121522	PABPC4L	non_synonymous_codon	c.827G>A	p.S276N	0.52	0	45			1.14016	1.92159
4	151000309	DCLK2	non_synonymous_codon	c.130C>A	p.L44I	0.5	0	49			1.14655	1.37846
5	140553488	PCDHB7	non_synonymous_codon	c.1072G>A	p.E358K	0.27	0	35			0.606067	0.194355
5	175816340	HIGD2A	non_synonymous_codon	c.163G>T	p.A55S	0.47	0	49			1.04405	15.4683
5	179251300	SQSTM1	non_synonymous_codon	c.650G>A	p.R217H	0.43	0	66			0.97943	38.4831
6	100965942	ASCC3	non_synonymous_codon	c.5852T>C	p.I1951T	0.47	0	45			1.04988	11.0422
6	126080617	HEY2	non_synonymous_codon	c.683C>T	p.T228M	0.41	0	43			0.907476	0.037566
6	144070126	PHACTR2	non_synonymous_codon	c.219A>C	p.L73F	0.41	0	44			0.920948	10.2718
7	21695506	DNAH11	non_synonymous_codon	c.5001C>A	p.D1667E	0.33	0	41			1.03822	4.17408
7	39649386	YAE1D1	non_synonymous_codon	c.422G>A	p.S141N	0.33	0	46			1.042	13.5995
7	92763691	SAMD9L	non_synonymous_codon	c.1594C>A	p.L532I	0.29	0	38			0.938198	4.40977
7	121756802	AASS	non_synonymous_codon	c.779T>A	p.V260E	0.28	0	54			0.92394	4.26067
8	24250832	ADAMDEC1	non_synonymous_codon	c.265C>G	p.L89V	0.51	0	46			1.18862	0.203587
9	33347710	NFX1	non_synonymous_codon	c.2474A>G	p.K825R	0.057	0	42			0.127645	11.2156
9	101552725	ANKS6	non_synonymous_codon	c.523C>A	p.P175T	0.4	0	60			0.873361	2.71904
10	75457455	AGAP5	non_synonymous_codon	c.59A>C	p.Q20P	0.058	0	47			0.131399	7.04692
11	118263544	UBE4A	non_synonymous_codon	c.3029A>G	p.D1010G	0.46	0	42			1.02634	10.2147
11	123865313	OR10G6	non_synonymous_codon	c.556C>T	p.R186W	0.37	0	53			0.806646	0
11	128781700	KCNJ5	non_synonymous_codon	c.532G>A	p.V178I	0.39	0	42	✔		0.866843	0.55527
12	47628898	PCED1B	non_synonymous_codon	c.52G>A	p.V18M	0.26	0	40			0.804425	0.202481
12	113836935	SDS	non_synonymous_codon	c.175C>T	p.H59Y	0.34	0	60			0.762757	0.408721
14	70925531	ADAM21	non_synonymous_codon	c.1315A>T	p.T439S	0.058	0	33			0.129495	0.024045
15	35196649	AQR	non_synonymous_codon	c.1889A>T	p.D630V	0.26	0	48			0.843096	15.4681
16	23767024	CHP2	non_synonymous_codon	c.110C>T	p.A37V	0.067	0	34			0.151811	1.1927
16	66956040	RRAD	non_synonymous_codon	c.866A>G	p.N289S	0.42	0	44			0.957338	0.200276
16	69148514	HAS3	non_synonymous_codon	c.1007G>A	p.R336H	0.11	0	34			0.239994	0.046976
16	87735456	FLJ00104	non_synonymous_codon	c.665G>T	p.W222L	0.36	0	50			0.814185	0.142219
18	14852452	ANKRD30B	non_synonymous_codon	c.4152C>A	p.N1384K	0.78	0	36			0.952398	0.050045
19	35996863	DMKN	non_synonymous_codon	c.1064T>C	p.F355S	0.39	0	39			0.869794	0.214859
20	34055250	CEP250	non_synonymous_codon	c.721C>T	p.R241W	0.43	0	42			0.962527	4.94952
20	49571815	DPM1	non_synonymous_codon	c.169A>G	p.N57D	0.45	0	40			1.0052	10.9651
22	20709527	FAM230A	non_synonymous_codon	c.1259A>C	p.N420T	0.52	0.07	43			0.714298	0.061481
X	77529113	CYSLTR1	non_synonymous_codon	c.131T>C	p.V44A	0.8	0	18			1.77285	5.42012
X	79698692	FAM46D	non_synonymous_codon	c.654G>C	p.L218F	0.91	0	31			2.0565	0

Indel Results:

Indel Likely Drivers:

No Indel Likely Drivers

CHR	START	GENE	EFFECT	cDNA_CHANGE	PROTEIN_CHANGE	TARGET_VAF	REFERENCE_DEPTH	TSG	CCF	TARGET_VAFCORRECT_VAF	GENE_TPM
3	8809437	OXTR	frameshift_variant	c.436delC	p.R146fs*61	0.385	57		0.94936	0.42	0.279616
4	87731112	PTPN13	frameshift_variant	c.7290_7300delGGGATTAATCA	p.G2431fs*4	0.382	50	✔	0.865809	0.41	16.6623
4	140811578	MAML3	inframe_codon_loss	c.1009_1011delAAG	p.K337delK	0.317	52		0.883513	0.4	5.69363

Rearrangement Results:

Rearranged Tumor Suppressor Genes:

gene1	gene2	svclass	brass_score
EPHB2	BACH2	translocation	45
AGAP1	HDAC4	inversion	43
_	HDAC4	inversion	29
_	NF2	translocation	43
TERT	TERT	deletion	5

Rearranged Oncogenes:

gene1	gene2	svclass	brass_score
AGAP1	HDAC4	inversion	43
_	HDAC4	inversion	29
TERT	TERT	deletion	5
COL4A3BP	ROS1	translocation	37
KSR2	KSR2	tandem-duplication	46

Calls by Numbers:

	SNVS	Coding SNVS	INDELS	Coding INDELS	#Coding/Mb	#Muts/Mb	REARR
I-H-108333-T2-2-D1-1	3575	44	490	3	1.57	1.40	61

Integrated Circos:

Mutational Signatures

END REPORT

Patient I-H-108333

View Patient in Leukgen

Individual DMP ID: P-0006237

Gender: MALE

Disease(s): UNDIFFERENTIATED SARCOMA (UNDIFS)

Part C Consent: True

Number of WGS Samples: 1

Number of RNAseq Samples: 1

CBio Portal Results:

Tumor_Sample_Barcode	Chromosome	Start_Position	Reference_Allele	Tumor_Seq_Allele2	Hugo_Symbol	VAF	Variant_Classification	HGVSp_Short
P-0006237-T04-IM6	3	178917478	G	A	PIK3CA	0.270423	Missense_Mutation	p.G118D

RNA Sample: I-H-108333-T2-1-R1-1

Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

Tissue Site: R Gluteal Mass

Days since birth at collection: 8029

Fusion Results:

High Confidence Fusions:

GENE1	GENE2	DESCRIPTION	SPAN_READS	SPLIT_READS	LEFTBREAK	RIGHTBREAK	CALLER_EFFECT	ANNOT_EFFECT	CALLER	NUM_CALLERS
MGA	NUTM1	oncogene,cancer,exon-exon	14	19	15:42054560:+	15:34640170:+	in-frame	in-frame	FUSIONCATCHER	3

GENE1	GENE2	DESCRIPTION	SPAN_READS	SPLIT_READS	LEFTBREAK	RIGHTBREAK	CALLER_EFFECT	ANNOT_EFFECT	CALLER	NUM_CALLERS
IGH@	IL3RA	known,cancer,m0,multi	3	1	14:106913401:-	X:1449932:+	---/intergenic	---/intergenic	FUSIONCATCHER	1

View RNAFUSIONS Report

Expression TSNE Results:

Bokeh Application

Overexpressed Cancer Genes:

Gene	Log Fold Change	Loc	Cancers
NUTM1	7.61806	15q14	lethal midline carcinoma
OLIG2	4.29052	21q22.11	T-ALL
MLF1	3.65278	3q25.1	AML
LRIG3	2.29114	12q14.1	NSCLC
SFRP4	2.16084	7p14.1	colorectal cancer, melanoma, SCC, gastric cancer, oesophageal SCC

WGS Sample: I-H-108333-T2-2-D1-1

Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

Tissue Site: R Gluteal Mass

Days since birth at collection: 8029

Normal used: I-H-108333-N2-1-D1-1

Median Coverage: 115

MSISensor HAS NOT BEEN RUN

Copy Number Results:

Tumor Purity: 0.9

Tumor Ploidy: 2.24

No Amplifications or Homozygous losses for Oncogenes or TSGs

SNV Results:

SNV Likely Drivers:

CHR	START	GENE	EFFECT	cDNA_CHANGE	PROTEIN_CHANGE	TARGET_VAF	REFERENCE_VAF	REFERENCE_DEPTH	Oncogene	TSG	CCF	GENE_TPM
3	178917478	PIK3CA	non_synonymous_codon	c.353G>A	p.G118D	0.35	0	37	✔		0.785316	9.70179

CHR	START	GENE	EFFECT	cDNA_CHANGE	PROTEIN_CHANGE	TARGET_VAF	REFERENCE_VAF	REFERENCE_DEPTH	Oncogene	TSG	CCF	GENE_TPM
1	35657838	SFPQ	non_synonymous_codon	c.813G>C	p.K271N	0.42	0	43		✔	0.930745	77.7173
1	43213986	LEPRE1	non_synonymous_codon	c.1723G>T	p.V575F	0.37	0	42			0.843369	17.4142
2	103321091	SLC9A2	non_synonymous_codon	c.1934G>A	p.R645Q	0.42	0	47			0.924928	1.04438
2	128263132	IWS1	non_synonymous_codon	c.347A>G	p.H116R	0.41	0	31			0.957338	8.2394
2	161052875	ITGB6	non_synonymous_codon	c.198A>T	p.L66F	0.43	0	39			0.96284	1.06111
2	170050292	LRP2	non_synonymous_codon	c.8809G>A	p.E2937K	0.39	0	45			0.859149	0.014024
2	174820961	SP3	splice_site_variant	c.280-1G>A	p.?	0.42	0	27			0.948306	19.1651
3	7456718	GRM7	non_synonymous_codon	c.1042G>A	p.A348T	0.45	0	39			0.994606	0.444721
3	178917478	PIK3CA	non_synonymous_codon	c.353G>A	p.G118D	0.35	0	37	✔		0.785316	9.70179
4	57344789	SRP72	non_synonymous_codon	c.799G>A	p.A267T	0.48	0	44			1.0941	22.1599
4	135121522	PABPC4L	non_synonymous_codon	c.827G>A	p.S276N	0.52	0	45			1.14016	1.92159
4	151000309	DCLK2	non_synonymous_codon	c.130C>A	p.L44I	0.5	0	49			1.14655	1.37846
5	140553488	PCDHB7	non_synonymous_codon	c.1072G>A	p.E358K	0.27	0	35			0.606067	0.194355
5	175816340	HIGD2A	non_synonymous_codon	c.163G>T	p.A55S	0.47	0	49			1.04405	15.4683
5	179251300	SQSTM1	non_synonymous_codon	c.650G>A	p.R217H	0.43	0	66			0.97943	38.4831
6	100965942	ASCC3	non_synonymous_codon	c.5852T>C	p.I1951T	0.47	0	45			1.04988	11.0422
6	126080617	HEY2	non_synonymous_codon	c.683C>T	p.T228M	0.41	0	43			0.907476	0.037566
6	144070126	PHACTR2	non_synonymous_codon	c.219A>C	p.L73F	0.41	0	44			0.920948	10.2718
7	21695506	DNAH11	non_synonymous_codon	c.5001C>A	p.D1667E	0.33	0	41			1.03822	4.17408
7	39649386	YAE1D1	non_synonymous_codon	c.422G>A	p.S141N	0.33	0	46			1.042	13.5995
7	92763691	SAMD9L	non_synonymous_codon	c.1594C>A	p.L532I	0.29	0	38			0.938198	4.40977
7	121756802	AASS	non_synonymous_codon	c.779T>A	p.V260E	0.28	0	54			0.92394	4.26067
8	24250832	ADAMDEC1	non_synonymous_codon	c.265C>G	p.L89V	0.51	0	46			1.18862	0.203587
9	33347710	NFX1	non_synonymous_codon	c.2474A>G	p.K825R	0.057	0	42			0.127645	11.2156
9	101552725	ANKS6	non_synonymous_codon	c.523C>A	p.P175T	0.4	0	60			0.873361	2.71904
10	75457455	AGAP5	non_synonymous_codon	c.59A>C	p.Q20P	0.058	0	47			0.131399	7.04692
11	118263544	UBE4A	non_synonymous_codon	c.3029A>G	p.D1010G	0.46	0	42			1.02634	10.2147
11	123865313	OR10G6	non_synonymous_codon	c.556C>T	p.R186W	0.37	0	53			0.806646	0
11	128781700	KCNJ5	non_synonymous_codon	c.532G>A	p.V178I	0.39	0	42	✔		0.866843	0.55527
12	47628898	PCED1B	non_synonymous_codon	c.52G>A	p.V18M	0.26	0	40			0.804425	0.202481
12	113836935	SDS	non_synonymous_codon	c.175C>T	p.H59Y	0.34	0	60			0.762757	0.408721
14	70925531	ADAM21	non_synonymous_codon	c.1315A>T	p.T439S	0.058	0	33			0.129495	0.024045
15	35196649	AQR	non_synonymous_codon	c.1889A>T	p.D630V	0.26	0	48			0.843096	15.4681
16	23767024	CHP2	non_synonymous_codon	c.110C>T	p.A37V	0.067	0	34			0.151811	1.1927
16	66956040	RRAD	non_synonymous_codon	c.866A>G	p.N289S	0.42	0	44			0.957338	0.200276
16	69148514	HAS3	non_synonymous_codon	c.1007G>A	p.R336H	0.11	0	34			0.239994	0.046976
16	87735456	FLJ00104	non_synonymous_codon	c.665G>T	p.W222L	0.36	0	50			0.814185	0.142219
18	14852452	ANKRD30B	non_synonymous_codon	c.4152C>A	p.N1384K	0.78	0	36			0.952398	0.050045
19	35996863	DMKN	non_synonymous_codon	c.1064T>C	p.F355S	0.39	0	39			0.869794	0.214859
20	34055250	CEP250	non_synonymous_codon	c.721C>T	p.R241W	0.43	0	42			0.962527	4.94952
20	49571815	DPM1	non_synonymous_codon	c.169A>G	p.N57D	0.45	0	40			1.0052	10.9651
22	20709527	FAM230A	non_synonymous_codon	c.1259A>C	p.N420T	0.52	0.07	43			0.714298	0.061481
X	77529113	CYSLTR1	non_synonymous_codon	c.131T>C	p.V44A	0.8	0	18			1.77285	5.42012
X	79698692	FAM46D	non_synonymous_codon	c.654G>C	p.L218F	0.91	0	31			2.0565	0

Indel Results:

Indel Likely Drivers:

No Indel Likely Drivers

CHR	START	GENE	EFFECT	cDNA_CHANGE	PROTEIN_CHANGE	TARGET_VAF	REFERENCE_DEPTH	TSG	CCF	TARGET_VAFCORRECT_VAF	GENE_TPM
3	8809437	OXTR	frameshift_variant	c.436delC	p.R146fs*61	0.385	57		0.94936	0.42	0.279616
4	87731112	PTPN13	frameshift_variant	c.7290_7300delGGGATTAATCA	p.G2431fs*4	0.382	50	✔	0.865809	0.41	16.6623
4	140811578	MAML3	inframe_codon_loss	c.1009_1011delAAG	p.K337delK	0.317	52		0.883513	0.4	5.69363

Rearrangement Results:

Rearranged Tumor Suppressor Genes:

gene1	gene2	svclass	brass_score
EPHB2	BACH2	translocation	45
AGAP1	HDAC4	inversion	43
_	HDAC4	inversion	29
_	NF2	translocation	43
TERT	TERT	deletion	5

Rearranged Oncogenes:

gene1	gene2	svclass	brass_score
AGAP1	HDAC4	inversion	43
_	HDAC4	inversion	29
TERT	TERT	deletion	5
COL4A3BP	ROS1	translocation	37
KSR2	KSR2	tandem-duplication	46

Calls by Numbers:

	SNVS	Coding SNVS	INDELS	Coding INDELS	#Coding/Mb	#Muts/Mb	REARR
I-H-108333-T2-2-D1-1	3575	44	490	3	1.57	1.40	61

Patient I-H-108333

View Patient in Leukgen

Individual DMP ID: P-0006237

Gender: MALE

Disease(s): UNDIFFERENTIATED SARCOMA (UNDIFS)

Part C Consent: True

Number of WGS Samples: 1

Number of RNAseq Samples: 1

CBio Portal Results:

RNA Sample: I-H-108333-T2-1-R1-1

Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

Tissue Site: R Gluteal Mass

Days since birth at collection: 8029

Fusion Results:

High Confidence Fusions:

View Rescued Fusions

View RNAFUSIONS Report

Expression TSNE Results:

Overexpressed Cancer Genes:

WGS Sample: I-H-108333-T2-2-D1-1

Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

Tissue Site: R Gluteal Mass

Days since birth at collection: 8029

Normal used: I-H-108333-N2-1-D1-1

Median Coverage: 115

MSISensor HAS NOT BEEN RUN

Copy Number Results:

Tumor Purity: 0.9

Tumor Ploidy: 2.24

View Raw Battenberg Images

No Amplifications or Homozygous losses for Oncogenes or TSGs

SNV Results:

SNV Likely Drivers:

View Passed SNV Coding Calls

Indel Results:

View Indel CCF

Indel Likely Drivers:

No Indel Likely Drivers

View Passed Coding Indel Calls

Rearrangement Results:

Rearranged Tumor Suppressor Genes:

Rearranged Oncogenes:

Calls by Numbers:

Integrated Circos:

Mutational Signatures

View 96 Mutational Context

END REPORT

Patient I-H-108333

View Patient in Leukgen

Individual DMP ID: P-0006237

Gender: MALE

Disease(s): UNDIFFERENTIATED SARCOMA (UNDIFS)

Part C Consent: True

Number of WGS Samples: 1

Number of RNAseq Samples: 1

CBio Portal Results:

RNA Sample: I-H-108333-T2-1-R1-1

Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

Tissue Site: R Gluteal Mass

Days since birth at collection: 8029

Fusion Results:

High Confidence Fusions:

View Rescued Fusions

View RNAFUSIONS Report

Expression TSNE Results:

Overexpressed Cancer Genes:

WGS Sample: I-H-108333-T2-2-D1-1

Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)

Tissue Site: R Gluteal Mass

Days since birth at collection: 8029

Normal used: I-H-108333-N2-1-D1-1

Median Coverage: 115

MSISensor HAS NOT BEEN RUN

Copy Number Results:

Tumor Purity: 0.9

Tumor Ploidy: 2.24

View Raw Battenberg Images

No Amplifications or Homozygous losses for Oncogenes or TSGs

SNV Results:

SNV Likely Drivers: